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PubMed1996

Amino-terminal sequence determinants for substrate recognition by platelet-derived growth factor receptor tyrosine kinase.

The specificity of protein kinases has been shown to be influenced by residues near the phosphoaccepting amino acid. To examine the determinants for platelet-derived growth factor receptor (PDGFR) tyrosine kinase specificity, a peptide library with three degenerate positions N-terminal to tyrosine was constructed. After reaction with PDGFR, the most abundant phosphopeptides were isolated by immunoaffinity chromatography on a column containing monoclonal anti-phosphotyrosine antibody. Further separation of bound phosphopeptides with reverse-phase HPLC led to the identification of three optimal substrates for PDGFR: Ala-Ala-Asn-Ile-Thr-Tyr-Ala-Ala-Arg-Arg-Gly, Ala-Ala-Asn-Arg-Thr-Tyr-Ala-Ala-Arg-Arg-Gly and Ala-Ala-Leu-Ile-Thr-Tyr-Ala-Ala-Arg-Arg-Gly, where underlined residues are in the degenerate positions of the peptide library. Kinetic analyses of the three individual peptides (synthesized separately) showed these peptides to be among the best reported substrates for PDGFR. Our results expand the range of amino acid residues that have been shown to serve as recognition elements for receptor tyrosine kinases.

Adenosine Triphosphate↗

PubMed1984

Structural comparisons of wild-type and nuclear transport-defective simian virus 40 large tumor antigens.

PARA(nT) is a defective SV40-adenovirus 7 hybrid virus which contains the entire early region of the SV40 genome and codes for the synthesis of SV40 large tumor antigen (T-ag). A transport-defective variant of this hybrid, PARA(cT), encodes T-ag that is not transported to the nucleus, but accumulates in the cytoplasm. The structures of T-ags extracted from wild-type (WT) SV40-, PARA(nT)-, and PARA(cT)-infected cells were compared by peptide mapping. All three types of T-ag underwent considerable degradation when extracted using Tris-buffered Nonidet P-40 at pH 8.0. The addition of 200 microM leupeptin to the extraction buffer significantly inhibited this degradation. Comparison of methionine-containing tryptic peptides revealed no differences among the T-ags, suggesting that their primary structures are similar or identical. Phosphopeptide mapping revealed no differences between SV40- and PARA(nT)-encoded T-ags. In contrast, PARA(cT)-encoded T-ag lacked a prominent phosphopeptide that was present in both of the others. The possible relevance of this difference in phosphorylation to the transport defect is discussed.

Adenoviridae↗

PubMed1988

Altered phosphorylation and activation of pp60c-src during fibroblast mitosis.

At least half the pp60c-src in NIH 3T3-derived c-src overexpresser cells in modified by novel threonine and, possibly, serine phosphorylation within its amino 16 kd region during mitosis. At the same time, the tryptic phosphopeptide containing Ser 17, the site of cyclic AMP-dependent phosphorylation, is either modified or dephosphorylated. While the amount of pp60c-src is not significantly altered, the in vitro-specific kinase activity of modified pp60c-src is enhanced 4- to 7-fold. Modified pp60c-src has the same tyrosine-containing tryptic phosphopeptides as pp60c-src from unsynchronized cells, indicating that activation is independent of Tyr 416/Tyr 527 phosphorylation. Electrophoretic mobility retardations indicated that endogenous pp60c-src and pp60v-src are similarly modified during mitosis. The modifications and enhanced activity disappear near the time of cell division. These results suggest that pp60c-src is regulated by and, in turn, may regulate mitosis-specific events in fibroblasts.

Animals↗

PubMed1987

Preganglionic stimulation increases the phosphorylation of tyrosine hydroxylase in the superior cervical ganglion by both cAMP-dependent and Ca2+-dependent protein kinases.

Electrical stimulation of the preganglionic cervical sympathetic trunk increases the phosphorylation of tyrosine hydroxylase in the superior cervical ganglion of the rat by a nicotinic mechanism and by a noncholinergic mechanism. We have measured the incorporation of [32P]Pi into specific tryptic phosphopeptides in tyrosine hydroxylase in order to identify the protein kinases that phosphorylate this enzyme in electrically stimulated ganglia. 32P-labeled tyrosine hydroxylase was isolated from the ganglion by immunoprecipitation and polyacrylamide gel electrophoresis and was subjected to tryptic hydrolysis. Seven tryptic peptides were resolved from these hydrolysates by two-dimensional thin-layer electrophoresis and chromatography. Preganglionic stimulation (20 Hz, 5 min) increased the incorporation of 32P into four of these peptides. In the presence of cholinergic antagonists, however, electrical stimulation increased the labeling of only one phosphopeptide. From a comparison of the effects of preganglionic stimulation with the effects of agonists that activate specific protein kinases, we conclude that electrical stimulation increases the phosphorylation of tyrosine hydroxylase by both a cAMP-dependent protein kinase and a Ca2+/calmodulin-dependent protein kinase. The nicotinic component of preganglionic stimulation appears to be mediated by a Ca2+/calmodulin-dependent protein kinase, while the noncholinergic component appears to be mediated by cAMP-dependent protein kinase. Although protein kinase C can phosphorylate tyrosine hydroxylase, this kinase does not appear to participate in the stimulation-induced phosphorylation of tyrosine hydroxylase in the superior cervical ganglion.

Animals↗

PubMed1992

Identification of protein phosphatase activities in maize seedlings.

Three phosphatases active on phosphocasein (PhosphoCasein Phosphatases) termed PCP-I, PCP-II and PCP-III were isolated from maize seedlings by DEAE-cellulose chromatography and were shown to display a different specificity toward a variety of phosphorylated substrates including pNPP, phosphohistones, phosphorylase a and several phosphopeptides containing either phosphoserine or phosphothreonine. PCP-I and PCP-II bind to heparin-Sepharose, retain a remarkable pNPP activity, are uncapable to dephosphorylate phosphorylase a, and display striking activity toward the acidic phosphopeptide AS[32P]EEEEE. They also by far prefer phosphoseryl peptide RRAS[32P]VA over its phosphothreonyl derivative and are unsensitive to okadaic acid up to 1 microM. These properties are not consistent with the belonging of PCP-I and -II to any of the known classes of protein phosphatases and suggest that they are acidic phosphatases. Conversely, PCP-III is essentially free of pNPP activity; it readily dephosphorylates phosphohistone H1 and phosphorylase a and it displays a striking preference toward the phosphothreonyl peptides (RRAT[32P]VA and RRREEET[32P]EEEAA), while the phosphoseryl peptides (RRAS[32P]VA and AS[32P]EEEEE) are very poor substrates of the enzyme. These properties together with the findings that PCP-III does not bind to heparin-Sepharose and is highly sensitive to okadaic acid (IC50 = 0.2 nM) allow to identify PCP-III with a protein phosphatase of the PP-2A class.

Amino Acid Sequence↗

PubMed1995

Dephosphorylation of abnormal sites of tau factor by protein phosphatases and its implication for Alzheimer's disease.

The abnormally phosphorylated forms of tau factor are major constituents of neurofibrillary tangles in Alzheimer's disease brain. In order to investigate protein phosphatases which are related to dephosphorylation of abnormal phosphorylation sites, we examined the dephosphorylation of tau factor phosphorylated by three proline-directed type protein kinases. Tau factor phosphorylated by cdc2 kinase and tau protein kinase II was dephosphorylated by the holoenzyme of protein phosphatase 2A and calcineurin, while either the catalytic subunit of protein phosphatase 2A or protein phosphatase 2C could not catalyze the dephosphorylation. From the kinetic analysis, we concluded that tau factors phosphorylated by the protein kinases serve as good substrates for protein phosphatase 2A and calcineurin. On the other hand, tau factor phosphorylated by glycogen synthase kinase 3 alpha was dephosphorylated by the catalytic subunit of protein phosphatases 2A as well as the holoenzyme of protein phosphatase 2A and calcineurin. It has been reported that serines 199, 202 and 396 according to the numbering of the longest human tau isoform are among the major abnormal phosphorylation sites of tau factor. We synthesized two phosphopeptides which contained phosphoserines 199 and 202 or phosphoserine 396 and prepared the polyclonal antibodies specific for the phosphopeptides. Using these antibodies, we confirmed that the holoenzyme of protein phosphatase 2A and calcineurin could dephosphorylate phosphoserines 199, 202 and 396 in tau factor. The catalytic subunit of protein phosphatase 2A could dephosphorylate phosphoserine 396 but not phosphoserines 199 and 202. Neurofibrillary tangles in Alzheimer's disease brain were immunostained with both antibodies but the normal neurons in the normal aged brains were not. The results suggest that protein phosphatase 2A and calcineurin can be involved in the dephosphorylation of abnormal phosphorylation sites in tau factor and that the dephosphorylation of phosphoserine 396 is differently regulated from phosphoserines 199 and 202.

Aged↗

PubMed1995

In vivo and in vitro phosphorylation of the human estrogen receptor.

We report here that the human estrogen receptor (hER) overexpressed in Sf9 insect cells is phosphorylated similarly to hER from the human MCF-7 mammary carcinoma cell line. The recombinant and native hER labeled to steady-state with [32P]phosphate were purified to homogeneity using specific DNA-affinity chromatography followed by SDS-gel electrophoresis. Resolution of the hER tryptic digests by reverse phase-high performance liquid chromatography revealed that five [32P]phosphopeptides from the hER expressed in the Sf9 cells had retention times identical to five of the seven [32P]phosphopeptides from the hER in MCF-7 cells. Uniquely, a dephosphorylation of a single 32P-labeled peptide occurred in response to estradiol treatment of MCF-7 cells. In vitro protein kinase assays with the purified recombinant hER revealed that the DNA-dependent protein kinase (DNA-PK) phosphorylated the receptor and induced a decrease in the receptor's mobility as demonstrated by SDS-gel electrophoresis. In contrast, protein kinases A and C did not phosphorylate the purified recombinant hER. These results suggest that in the process of becoming transcriptionally active the estrogen receptor undergoes a dephosphorylation after estrogen-binding and subsequent phosphorylations, in part by the DNA-PK.

Animals↗

PubMed2004

The long myosin light chain kinase is differentially phosphorylated during interphase and mitosis.

We have shown previously that the activity of the long myosin light chain kinase (MLCK) is cell cycle regulated with a decrease in specific activity during mitosis that can be restored following treatment with alkaline phosphatase. To better understand the role and significance of phosphorylation in regulating MLCK function during mitosis, we examined the phosphorylation state of in vivo derived MLCK. Phosphoamino acid analysis and phosphopeptide mapping demonstrate that the long MLCK is differentially phosphorylated on serine residues during interphase and mitosis with the majority of the phosphorylation sites located within the N-terminal IgG domain. Biochemical assays show that Aurora B binds and phosphorylates the IgG domain of the long MLCK. In addition, phosphopeptide maps of the endogenous full-length MLCK from mitotic cells and in vitro phosphorylated IgG domain demonstrate that Aurora B phosphorylates the same sites as those observed in vivo. Altogether, these studies suggest that the long MLCK may be a cellular target for Aurora B during mitosis.

Animals↗

PubMed2003

Synthesis of a radioactive thiol reagent, 1-S-[3H]carboxymethyl-dithiothreitol: identification of the phosphorylation sites by N-terminal peptide sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

A novel radioactive thiol reagent, 1-S-[3H]carboxymethyl-dithiothreitol (DTT-S-C[3H(2)]CO(2)H, [3H]CM-DTT), was designed and synthesized at the micromole level by reaction of dithiothreitol with tritiated iodoacetic acid (I-C[3H(2)].CO(2)H). The reaction progress was followed by reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The usefulness of the synthesized reagent was evaluated in a series of experimental approaches. (i) The synthetic phosphopeptide, NSVS(P)EEGRGDSV, was derivatized by [3H]CM-DTT separated from excess reagent by RP-HPLC. The extent of derivatization was quantitated in terms of the mol of P-Ser/mol of peptide by 3H counting, and the location of the phosphoserine was defined by the N-terminal Edman degradation sequence analysis as being the fourth amino acid residue from the N terminus. (ii) A sample of trypsin-digested alpha-casein was derivatized with [3H]CM-DTT, peptides were separated by RP-HPLC, and aliquots of each fraction were counted for 3H label within the peptide map which rapidly pinpointed the original four phosphoserine-containing peptides. This demonstrated the utility of the synthesized radioactive thiol agent in rapid purification and identification of phosphopeptides from HPLC peptide mapping of proteolytic digests of phosphoproteins. (iii) The [3H]CM-DTT was also used to determine the extent of phosphorylation of phosphoproteins both qualitatively by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography and quantitatively by 3H counting. The synthesized radioactive thiol reagent [3H]CM-DTT proved to be very efficient and sensitive and should be adaptable to a wide range of routinely utilized laboratory approaches in many fields of the biological sciences.

Binding Sites↗

PubMed2001

Evaluation of site-directed spin labeling for characterizing protein-ligand complexes using simulated restraints.

Simulation studies have been performed to evaluate the utility of site-directed spin labeling for determining the structures of protein-ligand complexes, given a known protein structure. Two protein-ligand complexes were used as model systems for these studies: a 1.9-A-resolution x-ray structure of a dihydrofolate reductase mutant complexed with methotrexate, and a 1.5-A-resolution x-ray structure of the V-Src tyrosine kinase SH2 domain complexed with a five-residue phosphopeptide. Nitroxide spin labels were modeled at five dihydrofolate reductase residue positions and at four SH2 domain residue positions. For both systems, after energy minimization, conformational ensembles of the spin-labeled residues were generated by simulated annealing while holding the remainder of the protein-ligand complex fixed. Effective distances, simulating those that could be obtained from (1)H-NMR relaxation measurements, were calculated between ligand protons and the spin labels. These were converted to restraints with several different levels of precision. Restrained simulated annealing calculations were then performed with the aim of reproducing target ligand-binding modes. The effects of incorporating a few supplementary short-range (< or =5.0 A) distance restraints were also examined. For the dihydrofolate reductase-methotrexate complex, the ligand-binding mode was reproduced reasonably well using relatively tight spin-label restraints, but methotrexate was poorly localized using loose spin-label restraints. Short-range and spin-label restraints proved to be complementary. For the SH2 domain-phosphopeptide complex without the short-range restraints, the peptide did not localize to the correct depth in the binding groove; nevertheless, the orientation and internal conformation of the peptide was reproduced moderately well. Use of the spin-label restraints in conjunction with the short-range restraints resulted in relatively well defined structural ensembles. These results indicate that restraints derived from site-directed spin labeling can contribute significantly to defining the orientations and conformations of bound ligands. Accurate ligand localization appears to require either a few supplementary short-range distance restraints, or relatively tight spin-label restraints, with at least one spin label positioned so that some of the restraints draw the ligand into the binding pocket in the latter case.

Binding Sites↗

PubMed1997

Identification of Raf-1 Ser621 kinase activity from NIH 3T3 cells as AMP-activated protein kinase.

Raf-1 is extensively phosphorylated on Ser621 in both quiescent and mitogen-stimulated cells. To identify the responsible kinase(s), cytosolic fractions of NIH 3T3 cells were analyzed for Ser621 peptide kinase activity. One major peak of activity was detected and identified as AMP-activated protein kinase (AMPK) by immunodepletion experiments. AMPK phosphorylated the catalytic domain of Raf-1, expressed in Escherichia coli as a soluble GST fusion protein, to generate a single tryptic [32P]phosphopeptide containing exclusively phospho-Ser621. AMPK also phosphorylated full-length, kinase-defective Raf-1 (K375M) to generate two [32P]phosphopeptides, one co-migrating with synthetic tryptic peptide containing phospho-Ser621 and the other with phospho-Ser259.

3T3 Cells↗

PubMed1997

A screening method of SH2 domain ligands and blockers using a solid phase binding.

We have developed a high throughput screening method for SH2 domain binding ligands and blockers. This method measures directly the binding of a 3H-labeled phosphopeptide derived from the sequence around tyrosine317 in the human Shc (SpYVNVK) to the SH2 domain of Grb2, which is precoated as glutathione S-transferase fusion proteins on solid phase. The optimum concentration for the fusion protein coating was 300 ng/100 microl/well for SH2 domain binding. Although an 8-h incubation at 4 degrees C for the coating of fusion protein was required to reach a maximum binding, even a 2-h coating produced 84% of the maximum binding. Saturation of ligand peptide binding in our assay system was observed at 10 pmol/well for the SH2 domain. However, 2 pmol/well showed consistent and reproducible results for the binding when the incubations were performed for 8 h at 4 degrees C. Competitive binding inhibition studies with various unlabeled phosphopeptides imply that the binding assay is highly specific to peptide sequences and able to screen possible ligands or blockers of signal transduction pathway mediated by Grb2 SH2 binding. In conclusion, our new method for SH2 domain binding is easy, rapid, and most of all inexpensive. These advantages over existing assay methods make this method especially suitable for a high throughput application, such as the screening for anticancer drug candidates.

Adaptor Proteins, Signal Transducing↗

PubMed2001

P1, a high mobility group-like protein is depressed in human breast adenocarcinoma.

Protein P1, which is a nuclear protein resembling high mobility group proteins, has been studied in human breast adenocarcinomas and compared to those from control tissue. The presence of the protein was confirmed by in vitro phosphorylation by casein kinase II and immunoblotting, using antibodies raised in rabbits against rat liver P1. The protein has been isolated by reverse phase HPLC chromatography which provides a more rapid method of purification requiring smaller amounts of material. The levels of P1 expression were investigated and it was found that there was a three-fold increase in the ratio of P1/histone H1 in normal breast tissue as compared to the neoplastic tissue. In two other malignant and non-malignant tissues studied, the level of P1 was also decreased in the malignant tissues. Thermolytic phosphopeptides of P1 from normal and malignant human breast tissues exhibited the same pattern, though when compared to the phosphopeptide pattern from rat tissue, differences were observed.

Adenocarcinoma↗

PubMed2000

Structural basis for specificity switching of the Src SH2 domain.

The Src SH2 domain binds pYEEI-containing phosphopeptides in an extended conformation with a hydrophobic pocket, which includes ThrEF1, binding Ile(pY +3). Mutating ThrEF1 to tryptophan switches specificity to an Asn(pY +2) requirement, yielding a biological mimic of the Grb2 SH2 domain. Here we show that the Src ThrEF1Trp SH2 domain mutant binds pYVNV phosphopeptides in a beta turn conformation, which, despite differing conformations of the interacting tryptophan, closely resembles the native Grb2/pYVNV cognate peptide binding mode. The ThrEF1Trp substitution therefore switches specificity by physically occluding the pTyr +3 binding pocket and by providing additional interaction surface area for Asn(pY +2). This demonstrates structurally how novel SH2 domain specificities may rapidly evolve through single amino acid substitutions and suggests how new signaling pathways may develop.

Adaptor Proteins, Signal Transducing↗

PubMed1989

Chemical characterization of bioactive peptides from in vivo digests of casein.

The in vivo formation of biologically active caseinopeptides was studied. It was proved that bioactive peptides were released in the small intestine of minipigs in the course of luminal digestion of diets containing bovine casein. An opioid peptide and a phosphopeptide were isolated from jejunal chyme and were chemically characterized. The opioid peptide has been identified as a fragment of beta-casein (60-70). This peptide, named beta-casomorphin-11, displayed substantial opioid activity in an opiate receptor-binding assay. The caseinophosphopeptide has been shown to be a fragment of alpha s1-casein (66-74). Casein-derived phosphopeptides exhibit a potent ability to form soluble complexes with Ca and trace elements. Evidence exists that casomorphins and caseinophosphopeptides participate in the regulation of nutrient entry.

Animals↗

PubMed1994

Characterization of the oligopeptides of Parmigiano-Reggiano cheese soluble in 120 g trichloroacetic acid/l.

The non-protein nitrogen (NPN) of samples of Parmigiano-Reggiano cheese ripened for 6 and 15 months was fractionated by ion-exchange chromatography on a Cu(2+)-Chelex column to separate oligopeptides from free amino acids. Peptide components were isolated by reversed-phase HPLC and identified by fast atom bombardment-mass spectrometry (FAB-MS). Only the NPN fraction of 6 month old cheese samples contained enough peptides to be further characterized. On the basis of FAB-MNS spectral results, 39 oligopeptides were identified, the main components being phosphopeptides. Two sets of both intact and partly dephosphorylated peptides, accounting for a total of 19 phosphopeptides, were formed by the hydrolysis of beta-casein and belonged to regions 1-20 and 6-28 of beta-casein. The formation and potential role of these peptides in cheese is discussed.

Amino Acid Sequence↗

PubMed1998

Identification of phosphorylation sites in proteins separated by polyacrylamide gel electrophoresis.

We report a fast, sensitive, and robust procedure for the identification of precise phosphorylation sites in proteins separated by polyacrylamide gel electrophoresis by a combination of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOF) and online capillary liquid chromatography electrospray tandem ion trap mass spectrometry (LC/ESI/MS/MS). With this procedure, a single phosphorylation site was identified on as little as 20 ng (500 fmol) of the baculovirus-expressed catalytic domain of myosin I heavy-chain kinase separated by gel electrophoresis. The phosphoprotein is digested in the gel with trypsin, and the resulting peptides are extracted with > 60% yield and analyzed by MALDI/TOF before and after digestion with a phosphatase to identify the phosphopeptides. The phosphopeptides are then separated and fragmented in an on-line LC/ESI ion trap mass spectrometer to identify the precise phosphorylation sites. This procedure eliminates any off-line HPLC separation and minimizes sample handling. The use of MALDI/TOF and LCQ, two types of mass spectrometers that are widely available to the biological community, will make this procedure readily accessible to biologists. We applied this technique to identify two autophosphorylation sites and to assign at least another 12 phosphorylation sites to two tryptic peptides in a series of experiments using a gel slice containing only 200 ng (3 pmol) of human double-stranded RNA-activated protein kinase expressed in a mutant strain of the yeast Saccharomyces cerevisiae.

Acanthamoeba↗

PubMed1998

Analysis of phospho- and glycopolypeptides with infrared matrix-assisted laser desorption and ionization.

The analytical characteristics of infrared (IR) matrix-assisted laser desorption and ionization (MALDI) were investigated for the analysis of phosphopeptides, a phosphopolypeptide, and glycopeptides. Two commercially available instruments, a high-resolution delayed extraction (DE) reflectron time-of-flight (RETOF) mass spectrometer and a high-power pulsed Er:YAG laser, were interfaced to produce a high-resolution MALDI-DE-RETOF instrument that is easy to use and can be switched between UV- and IR-MALDI mode within seconds. In the interface design, particular attention was paid to maintaining the same professional operating environment for the new IR-MALDI mode as exists for the commercial UV-MALDI mode. This instrument configuration facilitates comparative observation and investigation of the relative analytical merits of IR- and UV-MALDI. The results of studies of the tryptic alpha-casein phosphopeptides, RP1 (a Thr45-monophosphorylated congener of the recombinant protein hirudin variant 1), and fetuin Asn81 tryptic glycopeptides are presented. The elimination of labile substituents such as phosphoric acid and sialic acid is suppressed in IR-MALDI-RETOF mass spectrometry, with concomitant higher analyte ion yields. These results reflect the advantages that accrue from deposition of significantly less internal energy in the case of IR-MALDI.

Amino Acid Sequence↗